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S U M M A R YThe Zafarraya Basin is one of the intramountain Neogene basins of the Betic mountains (Southern Spain) located in one of the regions with the highest hazard level in the Iberian Peninsula. In this paper we use the indirect boundary element method (IBEM) to compute the 3-D ground motion of the Zafarraya Basin under incident P and S waves. We solve the linear system of equations obtained in the IBEM by using a partition matrix method that has been found more efficient than the classic L · U decomposition used in previous works. Our results show that the horizontal displacements are greatly amplified both in amplitude and duration in those components where direct motion exists (radial for P and SV waves, and transverse for SH waves). In any case, the other horizontal displacements where no direct motion exists are not negligible. The most important amplifications are produced at the south of the Zafarraya Basin, where two features characterize these sites: first the depth of the basin is the largest, and second, these locations are near the end of the basin where a very steep boundary exists. Some of the waves that have produced the increase in duration have been interpreted as surface waves, which in some cases provide characteristic polarization patterns.